Downsampling is the process of selecting a limited number of data points/events from a sample or gated population. A new Downsample Gate is created containing the selected subset of events, which can be used like any other gated subset or population node within FlowJo.
Downsampling is often a necessary prerequisite to algorithmic calculations like t-Distributed Stochastic Neighbor Embedding (tSNE), as reducing the number of events fed into an algorithm will decrease calculation speed and provide an output in a reasonable period of time.
FlowJo v10.1r7 and above use a Plugin mechanism for creating downsample gates. Plugins can be accessed and run through the Plugins menu (Workspace tab –> Populations band).
- Please see the Installing Plugins page for detailed information on how to obtain and setup FlowJo plugins.
- The DownSample plugin does not require R.
- Open FlowJo v10.1r7 or later.
- Select/highlight a gated population within the samples pane of the FlowJo workspace.
- Initiate DownSample from the Plugins menu (Workspace Tab –> Populations Band) .
- Enter the Number of events desired in the downsample gate.
- Name the downsample gate (optional) and click OK.
The DownSample plugin will randomly sample events from the selected parent subset and create a new child gate with the user entered name containing those events.
For more information on installing and running specific Plugins:
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